A consistent t(2;13) (q35;q14) translocation in alveolar RMS results in fusion between PAX3 or PAX7 genes with the FKHR factors. Using reverse transcription (RT)-PCR and fluorescence in situ hybridization (FISH) technique, we will investigate the presence of PAX3 (PAX7)/FKHR transcripts in a large number of alveolar RMS. Embryonal RMS on the other hand exhibits a reproducible loss of chromosomal material on chromosome 11p15.5. We have used oligonucleotide repeats at the tyrosine hydroxylase (TH) locus and investigated loss of heterozygosity (LOH) in 11 RMS and 13 non-RMS sarcomas in children and young adults. We found consistent LOH at the TH locus in all but one (botryoid) RMS. However, LOH was also detected in 2 nerve sheath tumors and one fibrosarcoma. We would like to extend our studies to include a larger sample of RMS and non-RMS tumors. Our preliminary findings however suggest, that although the RT-PCR detected fusion transcripts are specific for alveolar RMS, LOH at the 11p15.5 locus is present not only in embryonal RMS, but other tumors as well.